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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-05-05 Fri 07:24 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -383,7 +383,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 07:24</p>
<p class="date">Created: 2023-05-05 Fri 10:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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examples.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-05-05 Fri 07:24 -->
<!-- 2023-05-05 Fri 10:56 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -346,61 +346,61 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgd1bf383">1. Writing nuclear coordinates</a>
<li><a href="#orgb77321c">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org89bfed3">1.1. C</a></li>
<li><a href="#org46d5da5">1.2. Python</a></li>
<li><a href="#orgccd02c3">1.3. Fortran</a></li>
<li><a href="#org1951b29">1.1. C</a></li>
<li><a href="#org4d6b996">1.2. Python</a></li>
<li><a href="#orgff5cd72">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org99b27b9">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgd9e05d3">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org30c0192">2.1. Fortran</a>
<li><a href="#orgf523638">2.1. Fortran</a>
<ul>
<li><a href="#org10d745c">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org8b2b534">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org159c7a1">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org2cbb499">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org80a623f">2.1.5. Allocate memory</a></li>
<li><a href="#org4f60590">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org4a0e1c8">2.1.7. Read two-electron quantities</a>
<li><a href="#org1d9390c">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgc4eaf5c">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org115a696">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org5d919f4">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org3b2e374">2.1.5. Allocate memory</a></li>
<li><a href="#org644092d">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgaa319b3">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org5aabd62">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org06def01">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgb992b6e">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org7ba62ef">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org2c7803a">2.1.8. Compute the energy</a></li>
<li><a href="#org609a841">2.1.9. Terminate</a></li>
<li><a href="#org1f3771e">2.1.8. Compute the energy</a></li>
<li><a href="#org9f737ca">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org9d254f4">2.2. Python</a>
<li><a href="#org983a2a5">2.2. Python</a>
<ul>
<li><a href="#org236dacd">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org4f216e8">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org34e6dbc">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org7d2602e">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgc6a3f95">2.2.5. Read two-electron quantities</a>
<li><a href="#org48ad3eb">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org197c15c">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org6ab5870">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org75770e6">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgab7a0fe">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orge9a2abe">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org5ed5f4a">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org6210dca">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgd7d581b">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgbc6fa69">2.2.6. Compute the energy</a></li>
<li><a href="#org5aab5cb">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgcdd1b7c">3. Reading determinants</a>
<li><a href="#org0fbf991">3. Reading determinants</a>
<ul>
<li><a href="#orgb8c47dc">3.1. Fortran</a></li>
<li><a href="#org82eb594">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgd1bf383" class="outline-2">
<h2 id="orgd1bf383"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-orgb77321c" class="outline-2">
<h2 id="orgb77321c"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div class="outline-text-2" id="text-1">
<p>
Here is a demonstration of how to use TREXIO to write the nuclear
@ -410,8 +410,8 @@ as well as the necessary TREXIO functions to perform these actions.
</p>
</div>
<div id="outline-container-org89bfed3" class="outline-3">
<h3 id="org89bfed3"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org1951b29" class="outline-3">
<h3 id="org1951b29"><span class="section-number-3">1.1</span> C</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#include</span> <span style="color: #8b2252;">&lt;stdio.h&gt;</span>
@ -461,8 +461,8 @@ as well as the necessary TREXIO functions to perform these actions.
</div>
</div>
<div id="outline-container-org46d5da5" class="outline-3">
<h3 id="org46d5da5"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org4d6b996" class="outline-3">
<h3 id="org4d6b996"><span class="section-number-3">1.2</span> Python</h3>
<div class="outline-text-3" id="text-1-2">
<p>
This code uses the TREXIO Python binding to create a new TREXIO file named
@ -509,8 +509,8 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-orgccd02c3" class="outline-3">
<h3 id="orgccd02c3"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgff5cd72" class="outline-3">
<h3 id="orgff5cd72"><span class="section-number-3">1.3</span> Fortran</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">trexio_water</span>
@ -567,12 +567,12 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-org99b27b9" class="outline-2">
<h2 id="org99b27b9"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgd9e05d3" class="outline-2">
<h2 id="orgd9e05d3"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org30c0192" class="outline-3">
<h3 id="org30c0192"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgf523638" class="outline-3">
<h3 id="orgf523638"><span class="section-number-3">2.1</span> Fortran</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -618,8 +618,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org10d745c" class="outline-4">
<h4 id="org10d745c"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org1d9390c" class="outline-4">
<h4 id="org1d9390c"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-2-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
@ -634,8 +634,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org8b2b534" class="outline-4">
<h4 id="org8b2b534"><span class="section-number-4">2.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-orgc4eaf5c" class="outline-4">
<h4 id="orgc4eaf5c"><span class="section-number-4">2.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-2-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -651,8 +651,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-org159c7a1" class="outline-4">
<h4 id="org159c7a1"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org115a696" class="outline-4">
<h4 id="org115a696"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -666,8 +666,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-org2cbb499" class="outline-4">
<h4 id="org2cbb499"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org5d919f4" class="outline-4">
<h4 id="org5d919f4"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -681,8 +681,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-org80a623f" class="outline-4">
<h4 id="org80a623f"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org3b2e374" class="outline-4">
<h4 id="org3b2e374"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-2-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -694,8 +694,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org4f60590" class="outline-4">
<h4 id="org4f60590"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org644092d" class="outline-4">
<h4 id="org644092d"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -727,8 +727,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org4a0e1c8" class="outline-4">
<h4 id="org4a0e1c8"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgaa319b3" class="outline-4">
<h4 id="orgaa319b3"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -744,8 +744,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org5aabd62" class="outline-5">
<h5 id="org5aabd62"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgb992b6e" class="outline-5">
<h5 id="orgb992b6e"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -794,8 +794,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org06def01" class="outline-5">
<h5 id="org06def01"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org7ba62ef" class="outline-5">
<h5 id="org7ba62ef"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -839,8 +839,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org2c7803a" class="outline-4">
<h4 id="org2c7803a"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org1f3771e" class="outline-4">
<h4 id="org1f3771e"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-1-8">
<p>
When the orbitals are real, we can use
@ -886,8 +886,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org609a841" class="outline-4">
<h4 id="org609a841"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org9f737ca" class="outline-4">
<h4 id="org9f737ca"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-2-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -899,8 +899,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org9d254f4" class="outline-3">
<h3 id="org9d254f4"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org983a2a5" class="outline-3">
<h3 id="org983a2a5"><span class="section-number-3">2.2</span> Python</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">import</span> sys
@ -934,8 +934,8 @@ One needs to read from the TREXIO file:
</dl>
</div>
<div id="outline-container-org236dacd" class="outline-4">
<h4 id="org236dacd"><span class="section-number-4">2.2.1</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-org48ad3eb" class="outline-4">
<h4 id="org48ad3eb"><span class="section-number-4">2.2.1</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">filename</span> = sys.argv[1]
@ -945,8 +945,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org4f216e8" class="outline-4">
<h4 id="org4f216e8"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org197c15c" class="outline-4">
<h4 id="org197c15c"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-2-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">E_nn</span> = trexio.read_nucleus_repulsion(f)
@ -955,8 +955,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org34e6dbc" class="outline-4">
<h4 id="org34e6dbc"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org6ab5870" class="outline-4">
<h4 id="org6ab5870"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">n</span> = trexio.read_mo_num(f)
@ -965,8 +965,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org7d2602e" class="outline-4">
<h4 id="org7d2602e"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org75770e6" class="outline-4">
<h4 id="org75770e6"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_1e_int_core_hamiltonian(f):
@ -985,12 +985,12 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgc6a3f95" class="outline-4">
<h4 id="orgc6a3f95"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgab7a0fe" class="outline-4">
<h4 id="orgab7a0fe"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-5">
</div>
<div id="outline-container-orge9a2abe" class="outline-5">
<h5 id="orge9a2abe"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org6210dca" class="outline-5">
<h5 id="org6210dca"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-2-5-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_2e_int_eri(f):
@ -1020,8 +1020,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org5ed5f4a" class="outline-5">
<h5 id="org5ed5f4a"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orgd7d581b" class="outline-5">
<h5 id="orgd7d581b"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-2-5-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_rdm_2e(f):
@ -1043,8 +1043,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgbc6fa69" class="outline-4">
<h4 id="orgbc6fa69"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org5aab5cb" class="outline-4">
<h4 id="org5aab5cb"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-2-6">
<p>
When the orbitals are real, we can use
@ -1073,12 +1073,12 @@ E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
</div>
</div>
<div id="outline-container-orgcdd1b7c" class="outline-2">
<h2 id="orgcdd1b7c"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org0fbf991" class="outline-2">
<h2 id="org0fbf991"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgb8c47dc" class="outline-3">
<h3 id="orgb8c47dc"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org82eb594" class="outline-3">
<h3 id="org82eb594"><span class="section-number-3">3.1</span> Fortran</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -1157,7 +1157,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 07:24</p>
<p class="date">Created: 2023-05-05 Fri 10:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-05-05 Fri 07:24 -->
<!-- 2023-05-05 Fri 10:56 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -383,7 +383,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 07:24</p>
<p class="date">Created: 2023-05-05 Fri 10:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-05-05 Fri 07:24 -->
<!-- 2023-05-05 Fri 10:56 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Motivation</title>
@ -384,7 +384,7 @@ still lacking, and the purpose of the TREXIO library is to fill this gap.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 07:24</p>
<p class="date">Created: 2023-05-05 Fri 10:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-05-05 Fri 07:24 -->
<!-- 2023-05-05 Fri 10:56 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>The TREXIO library</title>
@ -346,19 +346,19 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgde54ba8">1. Format specification</a>
<li><a href="#orgdbb42b2">1. Format specification</a>
<ul>
<li><a href="#orgac90981">1.1. Organization of the data</a></li>
<li><a href="#org1f52fd5">1.2. Data types</a></li>
<li><a href="#org27ab3fb">1.1. Organization of the data</a></li>
<li><a href="#org13de2d5">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orge5fc1cc">2. The TREXIO library</a>
<li><a href="#org19eb35f">2. The TREXIO library</a>
<ul>
<li><a href="#orgc502b12">2.1. The front-end</a></li>
<li><a href="#org5daaef6">2.2. The back-end</a></li>
<li><a href="#orgf025038">2.3. Supported languages</a></li>
<li><a href="#org08f1a1f">2.4. Source code generation and documentation</a></li>
<li><a href="#org82ad967">2.5. Availability</a></li>
<li><a href="#orgd53e2ec">2.1. The front-end</a></li>
<li><a href="#org5aa982b">2.2. The back-end</a></li>
<li><a href="#org68b3340">2.3. Supported languages</a></li>
<li><a href="#orgcc05a0a">2.4. Source code generation and documentation</a></li>
<li><a href="#org1cebcb5">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgde54ba8" class="outline-2">
<h2 id="orgde54ba8"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-orgdbb42b2" class="outline-2">
<h2 id="orgdbb42b2"><span class="section-number-2">1</span> Format specification</h2>
<div class="outline-text-2" id="text-1">
</td>
<td>
@ -388,8 +388,8 @@ calculation are stored.
</p>
</div>
<div id="outline-container-orgac90981" class="outline-3">
<h3 id="orgac90981"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org27ab3fb" class="outline-3">
<h3 id="org27ab3fb"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div class="outline-text-3" id="text-1-1">
<p>
The data in TREXIO are organized into <b>groups</b>, each containing
@ -405,8 +405,8 @@ number of nuclei.
</div>
</div>
<div id="outline-container-org1f52fd5" class="outline-3">
<h3 id="org1f52fd5"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org13de2d5" class="outline-3">
<h3 id="org13de2d5"><span class="section-number-3">1.2</span> Data types</h3>
<div class="outline-text-3" id="text-1-2">
<p>
So that TREXIO can be used in any language, we use a limited number
@ -473,8 +473,8 @@ with the same name suffixed by <code>_im</code>.
</div>
</div>
<div id="outline-container-orge5fc1cc" class="outline-2">
<h2 id="orge5fc1cc"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org19eb35f" class="outline-2">
<h2 id="org19eb35f"><span class="section-number-2">2</span> The TREXIO library</h2>
<div class="outline-text-2" id="text-2">
</td>
<td>
@ -497,8 +497,8 @@ interface between the library and the physical storage.
</p>
</div>
<div id="outline-container-orgc502b12" class="outline-3">
<h3 id="orgc502b12"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgd53e2ec" class="outline-3">
<h3 id="orgd53e2ec"><span class="section-number-3">2.1</span> The front-end</h3>
<div class="outline-text-3" id="text-2-1">
<p>
By using the TREXIO library, users can store and extract data in a
@ -539,8 +539,8 @@ made are safe.
</div>
</div>
<div id="outline-container-org5daaef6" class="outline-3">
<h3 id="org5daaef6"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org5aa982b" class="outline-3">
<h3 id="org5aa982b"><span class="section-number-3">2.2</span> The back-end</h3>
<div class="outline-text-3" id="text-2-2">
<p>
At present, TREXIO supports two back-ends: one relying only on the
@ -610,8 +610,8 @@ repositories.
</div>
</div>
<div id="outline-container-orgf025038" class="outline-3">
<h3 id="orgf025038"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org68b3340" class="outline-3">
<h3 id="org68b3340"><span class="section-number-3">2.3</span> Supported languages</h3>
<div class="outline-text-3" id="text-2-3">
<p>
One of the main benefits of using C as the interface for a library is
@ -668,8 +668,8 @@ via the Binder platform.
</div>
<div id="outline-container-org08f1a1f" class="outline-3">
<h3 id="org08f1a1f"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-orgcc05a0a" class="outline-3">
<h3 id="orgcc05a0a"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div class="outline-text-3" id="text-2-4">
<p>
Source code generation is a valuable technique that can significantly
@ -723,8 +723,8 @@ regardless of their programming skills.
</div>
</div>
<div id="outline-container-org82ad967" class="outline-3">
<h3 id="org82ad967"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org1cebcb5" class="outline-3">
<h3 id="org1cebcb5"><span class="section-number-3">2.5</span> Availability</h3>
<div class="outline-text-3" id="text-2-5">
<p>
The TREXIO library is designed to be portable and easy to install
@ -754,7 +754,7 @@ are available in Ubuntu 23.04.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 07:24</p>
<p class="date">Created: 2023-05-05 Fri 10:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-05-05 Fri 07:23 -->
<!-- 2023-05-05 Fri 10:56 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -324,25 +324,25 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgb4fdca2">1. Template for HDF5 definitions</a></li>
<li><a href="#orgc36c137">2. Template for HDF5 structures</a></li>
<li><a href="#org40ed074">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orga363ad3">4. Template for HDF5 has a group</a></li>
<li><a href="#org33eceb8">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org41bf8c6">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgac9b6f9">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org345d427">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org8959415">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org6319d95">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orga74081e">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orga869654">12. Source code for the determinant part</a></li>
<li><a href="#org20f41f5">13. Helper functions</a></li>
<li><a href="#org87b6ece">1. Template for HDF5 definitions</a></li>
<li><a href="#org890811c">2. Template for HDF5 structures</a></li>
<li><a href="#orgfb8cd0e">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgd4f6b00">4. Template for HDF5 has a group</a></li>
<li><a href="#org6e61b1b">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orge4d4c24">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org69efba7">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org082a16c">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org6792bb3">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgc39800b">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org63632e0">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgb52a241">12. Source code for the determinant part</a></li>
<li><a href="#org37d4e53">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgb4fdca2" class="outline-2">
<h2 id="orgb4fdca2"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org87b6ece" class="outline-2">
<h2 id="org87b6ece"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgc36c137" class="outline-2">
<h2 id="orgc36c137"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org890811c" class="outline-2">
<h2 id="org890811c"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div class="outline-text-2" id="text-2">
<p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org40ed074" class="outline-2">
<h2 id="org40ed074"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgfb8cd0e" class="outline-2">
<h2 id="orgfb8cd0e"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orga363ad3" class="outline-2">
<h2 id="orga363ad3"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgd4f6b00" class="outline-2">
<h2 id="orgd4f6b00"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org33eceb8" class="outline-2">
<h2 id="org33eceb8"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org6e61b1b" class="outline-2">
<h2 id="org6e61b1b"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org41bf8c6" class="outline-2">
<h2 id="org41bf8c6"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orge4d4c24" class="outline-2">
<h2 id="orge4d4c24"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -770,8 +770,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgac9b6f9" class="outline-2">
<h2 id="orgac9b6f9"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org69efba7" class="outline-2">
<h2 id="org69efba7"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org345d427" class="outline-2">
<h2 id="org345d427"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org082a16c" class="outline-2">
<h2 id="org082a16c"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div class="outline-text-2" id="text-8">
<p>
Chunked I/O in HDF5 for <code>buffered</code> data.
@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org8959415" class="outline-2">
<h2 id="org8959415"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org6792bb3" class="outline-2">
<h2 id="org6792bb3"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org6319d95" class="outline-2">
<h2 id="org6319d95"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgc39800b" class="outline-2">
<h2 id="orgc39800b"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-orga74081e" class="outline-2">
<h2 id="orga74081e"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org63632e0" class="outline-2">
<h2 id="org63632e0"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-11">
<p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-orga869654" class="outline-2">
<h2 id="orga869654"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orgb52a241" class="outline-2">
<h2 id="orgb52a241"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-12">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org20f41f5" class="outline-2">
<h2 id="org20f41f5"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org37d4e53" class="outline-2">
<h2 id="org37d4e53"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1842,7 +1842,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 07:23</p>
<p class="date">Created: 2023-05-05 Fri 10:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org17ccb6f">1. Template for group-related structures in text back end</a></li>
<li><a href="#org5505aae">2. Template for general structure in text back end</a></li>
<li><a href="#org3a5e6f1">3. Initialize function (constant part)</a></li>
<li><a href="#org7ade52e">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgee3fc62">5. Flush function (templated part)</a></li>
<li><a href="#org84af45d">6. Template for text read a group</a></li>
<li><a href="#orgc81cb8b">7. Template for text has a group</a></li>
<li><a href="#org922ae37">8. Template for text flush a group</a></li>
<li><a href="#orgec65eb0">9. Template for text free memory</a></li>
<li><a href="#org1599ae0">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org001a998">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgbcd4fdf">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org4f01966">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgbbab33a">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org7196b49">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org2f53c0e">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org7e9da88">17. Source code for the determinant part</a></li>
<li><a href="#org65a2554">1. Template for group-related structures in text back end</a></li>
<li><a href="#org4966af7">2. Template for general structure in text back end</a></li>
<li><a href="#orgee90411">3. Initialize function (constant part)</a></li>
<li><a href="#orgdf5f4f2">4. Deinitialize function (templated part)</a></li>
<li><a href="#org19f17bb">5. Flush function (templated part)</a></li>
<li><a href="#orgc473536">6. Template for text read a group</a></li>
<li><a href="#org98ac0a7">7. Template for text has a group</a></li>
<li><a href="#orgeb6e345">8. Template for text flush a group</a></li>
<li><a href="#org2eb8bd9">9. Template for text free memory</a></li>
<li><a href="#orga91af63">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgce55a55">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgb5dcf87">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org5c82b36">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgb582c22">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org1c799e7">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgcf052cc">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org15604b2">17. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -362,8 +362,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org17ccb6f" class="outline-2">
<h2 id="org17ccb6f"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org65a2554" class="outline-2">
<h2 id="org65a2554"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org5505aae" class="outline-2">
<h2 id="org5505aae"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org4966af7" class="outline-2">
<h2 id="org4966af7"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div class="outline-text-2" id="text-2">
<p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org3a5e6f1" class="outline-2">
<h2 id="org3a5e6f1"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgee90411" class="outline-2">
<h2 id="orgee90411"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span>
@ -597,8 +597,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org7ade52e" class="outline-2">
<h2 id="org7ade52e"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgdf5f4f2" class="outline-2">
<h2 id="orgdf5f4f2"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -620,8 +620,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-orgee3fc62" class="outline-2">
<h2 id="orgee3fc62"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org19f17bb" class="outline-2">
<h2 id="org19f17bb"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -644,8 +644,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org84af45d" class="outline-2">
<h2 id="org84af45d"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgc473536" class="outline-2">
<h2 id="orgc473536"><span class="section-number-2">6</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -871,8 +871,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
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<h2 id="orgc81cb8b"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org98ac0a7" class="outline-2">
<h2 id="org98ac0a7"><span class="section-number-2">7</span> Template for text has a group</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -912,8 +912,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org922ae37" class="outline-2">
<h2 id="org922ae37"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orgeb6e345" class="outline-2">
<h2 id="orgeb6e345"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -977,8 +977,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgec65eb0" class="outline-2">
<h2 id="orgec65eb0"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org2eb8bd9" class="outline-2">
<h2 id="org2eb8bd9"><span class="section-number-2">9</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-9">
<p>
Memory is allocated when reading. The following function frees memory.
@ -1047,8 +1047,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org1599ae0" class="outline-2">
<h2 id="org1599ae0"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orga91af63" class="outline-2">
<h2 id="orga91af63"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1111,8 +1111,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org001a998" class="outline-2">
<h2 id="org001a998"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgce55a55" class="outline-2">
<h2 id="orgce55a55"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1208,8 +1208,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgbcd4fdf" class="outline-2">
<h2 id="orgbcd4fdf"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgb5dcf87" class="outline-2">
<h2 id="orgb5dcf87"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-12">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1310,8 +1310,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org4f01966" class="outline-2">
<h2 id="org4f01966"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org5c82b36" class="outline-2">
<h2 id="org5c82b36"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1385,8 +1385,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgbbab33a" class="outline-2">
<h2 id="orgbbab33a"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgb582c22" class="outline-2">
<h2 id="orgb582c22"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-14">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1676,8 +1676,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org7196b49" class="outline-2">
<h2 id="org7196b49"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org1c799e7" class="outline-2">
<h2 id="org1c799e7"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div class="outline-text-2" id="text-15">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
@ -1907,8 +1907,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org2f53c0e" class="outline-2">
<h2 id="org2f53c0e"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgcf052cc" class="outline-2">
<h2 id="orgcf052cc"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-16">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1936,8 +1936,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org7e9da88" class="outline-2">
<h2 id="org7e9da88"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org15604b2" class="outline-2">
<h2 id="org15604b2"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-17">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2129,7 +2129,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 07:23</p>
<p class="date">Created: 2023-05-05 Fri 10:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2023-05-05 Fri 07:24 -->
<!-- 2023-05-05 Fri 10:56 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Data stored in TREXIO</title>
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9cb3921">1. Metadata (metadata group)</a></li>
<li><a href="#org8e72032">2. System</a>
<li><a href="#orga02bc06">1. Metadata (metadata group)</a></li>
<li><a href="#org0599ee7">2. System</a>
<ul>
<li><a href="#org1613910">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org61d39fe">2.2. Cell (cell group)</a></li>
<li><a href="#orgce86b75">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgdcb53ed">2.4. Electron (electron group)</a></li>
<li><a href="#orgfbf81f7">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgd676562">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org198b824">2.2. Cell (cell group)</a></li>
<li><a href="#orgacf2439">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org2bb4266">2.4. Electron (electron group)</a></li>
<li><a href="#orged057c0">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org196e8d2">3. Basis functions</a>
<li><a href="#orge5b66b2">3. Basis functions</a>
<ul>
<li><a href="#orgc0f3f1c">3.1. Basis set (basis group)</a>
<li><a href="#orga0ff0a4">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgca8d913">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org79c6672">3.1.2. Plane waves</a></li>
<li><a href="#orgeb8efcd">3.1.3. Data definitions</a></li>
<li><a href="#org6af085b">3.1.4. Example</a></li>
<li><a href="#org635b629">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orga47d6d2">3.1.2. Plane waves</a></li>
<li><a href="#org4f6dea6">3.1.3. Data definitions</a></li>
<li><a href="#org14be6d0">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#orgb5841c2">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org12467f4">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orge0ae08e">3.2.1. Example</a></li>
<li><a href="#org2cd8ff7">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org3b31a21">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org59886ac">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org332b63f">4. Orbitals</a>
<li><a href="#orgf69554c">4. Orbitals</a>
<ul>
<li><a href="#orgc53e7eb">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgf9f1b2b">4.1. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">4.1.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">4.1.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org4045f98">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgdc8ba75">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orga28d47c">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org61e257d">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org9c285d6">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org6d8f47b">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org1d52fba">5. Multi-determinant information</a>
<li><a href="#org5e74be7">5. Multi-determinant information</a>
<ul>
<li><a href="#orgd3586fa">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org9309407">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org12c69ea">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org26ff340">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org5990004">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org73a74ef">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org02ddfd0">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org9b96610">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org08838cd">6. Correlation factors</a>
<li><a href="#orge213808">6. Correlation factors</a>
<ul>
<li><a href="#orga7697dd">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org4320391">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgec8b4ff">6.1.1. CHAMP</a></li>
<li><a href="#orgc9f5362">6.1.2. Mu</a></li>
<li><a href="#org5ee9fd8">6.1.3. Table of values</a></li>
<li><a href="#org156a12f">6.1.1. CHAMP</a></li>
<li><a href="#org4db1cb2">6.1.2. Mu</a></li>
<li><a href="#org1a380d9">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org88b5d83">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgc3d77a5">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -422,8 +422,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
library is written in C.
</p>
<div id="outline-container-org9cb3921" class="outline-2">
<h2 id="org9cb3921"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orga02bc06" class="outline-2">
<h2 id="orga02bc06"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect TREXIO files to be archived in open-data repositories,
@ -433,7 +433,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org446bb00" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1c4010e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -516,19 +516,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-org8e72032" class="outline-2">
<h2 id="org8e72032"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org0599ee7" class="outline-2">
<h2 id="org0599ee7"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org1613910" class="outline-3">
<h3 id="org1613910"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgd676562" class="outline-3">
<h3 id="orgd676562"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div class="outline-text-3" id="text-2-1">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="org9a95ce8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb2e139b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -595,15 +595,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org61d39fe" class="outline-3">
<h3 id="org61d39fe"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org198b824" class="outline-3">
<h3 id="org198b824"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div class="outline-text-3" id="text-2-2">
<p>
3 Lattice vectors to define a box containing the system, for example
used in periodic calculations.
</p>
<table id="orgf3358ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org08a93e8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -677,15 +677,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-orgce86b75" class="outline-3">
<h3 id="orgce86b75"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-orgacf2439" class="outline-3">
<h3 id="orgacf2439"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<p>
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
</p>
<table id="org571cd01" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc2d8939" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -724,8 +724,8 @@ defined in this group.
</div>
</div>
<div id="outline-container-orgdcb53ed" class="outline-3">
<h3 id="orgdcb53ed"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org2bb4266" class="outline-3">
<h3 id="org2bb4266"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div class="outline-text-3" id="text-2-4">
<p>
The chemical system consists of nuclei and electrons, where the
@ -744,7 +744,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org9dd2b06" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf681522" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -790,8 +790,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgfbf81f7" class="outline-3">
<h3 id="orgfbf81f7"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orged057c0" class="outline-3">
<h3 id="orged057c0"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div class="outline-text-3" id="text-2-5">
<p>
This group contains information about excited states. Since only a
@ -808,7 +808,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="org3283171" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7bfdba4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -869,16 +869,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org196e8d2" class="outline-2">
<h2 id="org196e8d2"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orge5b66b2" class="outline-2">
<h2 id="orge5b66b2"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgc0f3f1c" class="outline-3">
<h3 id="orgc0f3f1c"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orga0ff0a4" class="outline-3">
<h3 id="orga0ff0a4"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div class="outline-text-3" id="text-3-1">
</div>
<div id="outline-container-orgca8d913" class="outline-4">
<h4 id="orgca8d913"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org635b629" class="outline-4">
<h4 id="org635b629"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div class="outline-text-4" id="text-3-1-1">
<p>
We consider here basis functions centered on nuclei. Hence, it is
@ -932,8 +932,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org79c6672" class="outline-4">
<h4 id="org79c6672"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-orga47d6d2" class="outline-4">
<h4 id="orga47d6d2"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
A plane wave is defined as
@ -954,10 +954,10 @@ plane waves.
</div>
</div>
<div id="outline-container-orgeb8efcd" class="outline-4">
<h4 id="orgeb8efcd"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-org4f6dea6" class="outline-4">
<h4 id="org4f6dea6"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="org0a361e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc2aea17" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1066,8 +1066,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org6af085b" class="outline-4">
<h4 id="org6af085b"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org14be6d0" class="outline-4">
<h4 id="org14be6d0"><span class="section-number-4">3.1.4</span> Example</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1145,8 +1145,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgb5841c2" class="outline-3">
<h3 id="orgb5841c2"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org12467f4" class="outline-3">
<h3 id="org12467f4"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div class="outline-text-3" id="text-3-2">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -1180,7 +1180,7 @@ where \(Z_\text{eff}\) is the effective nuclear charge of the center.
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="orge3d97ef" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orged73b30" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1284,8 +1284,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-orge0ae08e" class="outline-4">
<h4 id="orge0ae08e"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org2cd8ff7" class="outline-4">
<h4 id="org2cd8ff7"><span class="section-number-4">3.2.1</span> Example</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -1348,8 +1348,8 @@ power = [
</div>
</div>
<div id="outline-container-org3b31a21" class="outline-3">
<h3 id="org3b31a21"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org59886ac" class="outline-3">
<h3 id="org59886ac"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div class="outline-text-3" id="text-3-3">
<p>
In some applications, such as DFT calculations, integrals have to
@ -1364,7 +1364,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
Feel free to submit a PR if you find missing options/functionalities.
</p>
<table id="org9ef2a82" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org93dd7c7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,12 +1481,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-org332b63f" class="outline-2">
<h2 id="org332b63f"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orgf69554c" class="outline-2">
<h2 id="orgf69554c"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orgc53e7eb" class="outline-3">
<h3 id="orgc53e7eb"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgf9f1b2b" class="outline-3">
<h3 id="orgf9f1b2b"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div class="outline-text-3" id="text-4-1">
<p>
AOs are defined as
@ -1567,7 +1567,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org0d7ea90" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfea7199" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1619,7 +1619,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-orgf830d71" class="outline-4">
<div id="outline-container-orgb885696" class="outline-4">
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_one_e">
<ul class="org-ul">
@ -1637,7 +1637,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgea63df0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb71a8f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1732,7 +1732,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgb0013d0" class="outline-4">
<div id="outline-container-org39cca40" class="outline-4">
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_two_e">
<p>
@ -1758,7 +1758,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org5fbcc4a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4ff02ee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,10 +1826,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org4045f98" class="outline-3">
<h3 id="org4045f98"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgdc8ba75" class="outline-3">
<h3 id="orgdc8ba75"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orga6f879a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org154a839" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,8 +1916,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-orga28d47c" class="outline-4">
<h4 id="orga28d47c"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org9c285d6" class="outline-4">
<h4 id="org9c285d6"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-1">
<p>
The operators as the same as those defined in the
@ -1925,7 +1925,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org3033ef9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org34866e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2020,8 +2020,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org61e257d" class="outline-4">
<h4 id="org61e257d"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org6d8f47b" class="outline-4">
<h4 id="org6d8f47b"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-2">
<p>
The operators are the same as those defined in the
@ -2029,7 +2029,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org056a475" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org947c399" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2098,12 +2098,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org1d52fba" class="outline-2">
<h2 id="org1d52fba"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org5e74be7" class="outline-2">
<h2 id="org5e74be7"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgd3586fa" class="outline-3">
<h3 id="orgd3586fa"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org5990004" class="outline-3">
<h3 id="org5990004"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div class="outline-text-3" id="text-5-1">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -2145,7 +2145,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="orgd061a7b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga424add" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2191,8 +2191,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org9309407" class="outline-3">
<h3 id="org9309407"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org73a74ef" class="outline-3">
<h3 id="org73a74ef"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div class="outline-text-3" id="text-5-2">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -2214,7 +2214,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org207358d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org67f1aaa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2260,8 +2260,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org12c69ea" class="outline-3">
<h3 id="org12c69ea"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org02ddfd0" class="outline-3">
<h3 id="org02ddfd0"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div class="outline-text-3" id="text-5-3">
<p>
The wave function may be expressed in terms of action of the cluster
@ -2332,7 +2332,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org725d8e2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga77b899" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2413,8 +2413,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org26ff340" class="outline-3">
<h3 id="org26ff340"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org9b96610" class="outline-3">
<h3 id="org9b96610"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div class="outline-text-3" id="text-5-4">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2486,7 +2486,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
</p>
<table id="orgcf20b56" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6739d8e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2617,12 +2617,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org08838cd" class="outline-2">
<h2 id="org08838cd"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orge213808" class="outline-2">
<h2 id="orge213808"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orga7697dd" class="outline-3">
<h3 id="orga7697dd"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org4320391" class="outline-3">
<h3 id="org4320391"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div class="outline-text-3" id="text-6-1">
<p>
The Jastrow factor is an $N$-electron function which multiplies the CI
@ -2647,8 +2647,8 @@ following:
</ul>
</div>
<div id="outline-container-orgec8b4ff" class="outline-4">
<h4 id="orgec8b4ff"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org156a12f" class="outline-4">
<h4 id="org156a12f"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div class="outline-text-4" id="text-6-1-1">
<p>
The first form of Jastrow factor is the one used in
@ -2749,8 +2749,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orgc9f5362" class="outline-4">
<h4 id="orgc9f5362"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org4db1cb2" class="outline-4">
<h4 id="org4db1cb2"><span class="section-number-4">6.1.2</span> Mu</h4>
<div class="outline-text-4" id="text-6-1-2">
<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -2847,10 +2847,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org5ee9fd8" class="outline-4">
<h4 id="org5ee9fd8"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org1a380d9" class="outline-4">
<h4 id="org1a380d9"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
<table id="orgd4c622b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7d3c4f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2954,8 +2954,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
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<h2 id="org88b5d83"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="orgc3d77a5"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2969,7 +2969,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3024,7 +3024,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 07:24</p>
<p class="date">Created: 2023-05-05 Fri 10:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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